I just got a Blue-Ray player and am thinking of upgrading my NetFlix account to Blue-Ray. It looks like it has an option to automatically select the blue-ray option when you add new things to your queue, but is there any way to have it go through my existing (lengthy) queue and replace in blue-ray versions wherever they are available?

There is no readily available way to update your Netflix DVD queue on the Netflix site, other than the available controls (add, remove, change order and change star ratings).

However, using their API you could (conceivably) write a script that will manipulate your queue in any way you want. You can schedule it to run periodically to scan all the DVDs in your queue, find out if they have a BluRay version and if so, replace the two.